This thesis describes an investigation of the mechanistic differences of hard and soft wheat varieties in the course of dough formation. These two classes of wheat exhibit dissimilar end-use, as hard wheat flour is known for its bread making attributes, whereas soft wheat flour is suitable for cake and cookie production. This difference is related to the grain hardness, protein content and property of gluten, in addition to chemical interactions that are occurring during dough making. Covalent and hydrophobic interactions, as well as hydrogen bond formation, are the main interactions that take place during dough mixing. However, the contribution of each interaction in dough formation of hard and soft wheat is not known. One variety of hard and one variety of soft wheat flour were mixed to their optimum hydration level (500 BU), as determined by farinograph. The extent of covalent interactions of gluten proteins during dough mixing was examined by monitoring changes in the solubility of flour proteins in a 2% Sodium Dodecyl Sulfate (SDS) media. Moreover, the contribution of thiol groups to covalent bond was examined by measuring the changes in the accessible thiols throughout the mixing. Lower extractability of proteins and accessible thiols of hard wheat dough, compared to soft wheat dough, indicated the predominant role of covalent interactions in hard wheat dough. The complementary results from Size Exclusion High Performance Liquid Chromatography (SE-HPLC) indicated that covalent interaction of hard wheat dough primarily occurs between Low Molecular Weight (LMW) and High Molecular Weight (HMW) gluten proteins, whereas this interaction mainly occurs among LMW proteins in soft wheat doughs. Fewer hydrophobic interactions in hard wheat dough in compare with soft wheat measured by Front-face fluorescence spectroscopy indicated that this interaction is more dominant in soft wheat dough. Study of the conformational change in secondary structure of protein (indirect approach to monitor hydrogen bond) by fourier transform infrared (FTIR) spectroscopy showed that β-sheets are formed in both varieties at their optimum dough strength. In hard wheat dough this structure resulted mainly from disulfide linkages, whereas in soft wheat dough this structure is more likely the result of hydrophobic interactions.

No description available.

No description available.

The use of cyanine dyes in bioanalytical applications has become a widely explored topic of interest in chemistry. Their ability to absorb and fluoresce in the UV-visible and near-infrared region of the electromagnetic spectrum benefits their use as imaging probes and fluorescent labels due to the reduced auto-fluorescence from biological molecules. The behavior of these dyes lies in their structure which consists of two nitrogen containing heterocycles joined by an electron deficient polymethine bridge that allows specific energy transitions to occur. The first portion of this work aims to explore dye functionality for analytical applications regarding the non-covalent labeling of bovine serum albumin. The second portion of the work explores dye interactions with human serum albumin in biological membrane mimetic environments using the ternary system of sodium dioctyl sulfosuccinate (AOT) in water and n-heptane.

This thesis described the modification of glassy carbon (GC) electrodes with aminophenyl (AP) films via in situ reduction of aminobenzene diazonium ions. The characterisation of the AP modified GC was conducted electrochemically by oxidation of the AP functionalities in acidic aqueous conditions. Ferricyanide and ruthenium hexamine redox probes were also used to investigate the blocking properties of the AP films. Before electrochemical oxidation of the AP functionalities, AP films were shown to have a nett positive charge at pH 7. After electrochemical oxidation in protic conditions, the film was either neutral or negatively charged. The preparation of diazonium cation terminated surface, which is termed 'sticky surface', by reaction of the AP modified electrodes with NaNO₂ in acidic condition, was investigated and the sticky surface was electrochemically characterised. More than one species was formed in the reaction of the AP film with NaNO₂. The reactions of sticky surface with aniline, citrate- and thiol-capped gold nanoparticles (Au-nps) were also studied. Spontaneous reaction of sticky surface with thiol-capped Au-nps had been achieved, and suggested that the reaction leads to the formation of Au–C bonds, via the loss of nitrogen. However, for the reaction of the sticky surface with citrate-capped Au-nps, it was unclear whether covalent bonding had been achieved. The reason for this was due to the possibility of an electrostatic interaction between the negatively charged citrate-capped Au-nps and the positively charged sticky surface. The stability of the sticky surface in acidic aqueous conditions was studied electrochemically and by reaction with thiol-capped Au-nps. It was found that the diazonium cations on the sticky surface are not stable over one hour in aqueous acidic conditions, or even in low temperature. The electro-catalytic activity of the thiol-capped Au-nps attached to the GC electrode via sticky surface towards the oxidation of ascorbic acid was briefly examined, and the surface was found to catalyse the oxidation reaction.

The focus of this thesis is the question of how non-covalent interactions affect chemical systems' electronic and structural properties. Non-covalent interactions can exhibit a range of binding strengths, from strong electrostatically-bound salt bridges or multiple hydrogen bonds to weak dispersion-bound complexes such as rare gas dimers or the benzene dimer. To determine the interaction energies (IE) of non-covalent interactions one generally takes the supermolecular approach as described by the equation \begin{equation} E_{IE} = E_{AB} - E_{A} - E_{B}, \end{equation} where subscripts A and B refer to two monomers and AB indicates the dimer. This interaction energy is the difference in energy between two monomers interacting at a single configuration compared to the completely non-interacting monomers at infinite separation. In this framework, positive interaction energies are repulsive or unfavorable while negative interaction energies signify a favorable interaction. We use prototype systems to understand systems with complex interactions such as π-π stacking in curved aromatic systems, three-body dispersion contributions to lattice energies and transition metal catalysts affect on transition state barrier heights. The current "gold standard" of computational chemistry is coupled-cluster theory with iterative single and double excitation and perturbative triple excitations [CCSD(T)].\cite{Lee:1995:47} Using CCSD(T) with large basis sets usually yields results that are in good agreement with experimental data.\cite{Shibasaki:2006:4397} CCSD(T) being very computational expensive forces us to use methods of a lower overall quality, but also much more tractable for some interesting problems. We must use the available CCSD(T) or experimental data available to benchmark lower quality methods in order to ensure that the low quality methods are providing and accurate description of the problem of interest. To investigate the effect of curvature on the nature of π-π interactions, we studied concave-convex dimers of corannulene and coronene in nested configurations. By imposing artificial curvature/planarity we were able to learn about the fundamental physics of π-π stacking in curved systems. To investigate these effects, it was necessary to benchmark low level methods for the interaction of large aromatic hydrocarbons. With the coronene and corannulene dimers being 60 and 72 atoms, respectively, they are outside the limits of tractability for a large number of computations at the level of CCSD(T). Therefore we must determine the most efficient and accurate method of describing the physics of these systems with a few benchmark computations. Using a few benchmark computations published by Janowski et al. (Ref. \cite{Janowski:2011:155}) we were able to benchmark four functionals (B3LYP, B97, M05-2X and M06-2X) as well as four dispersion corrections (-D2, -D3, -D3(BJ), and -XDM) and we found that B3LYP-D3(BJ) performed best. Using B3LYP-D3(BJ) we found that both corannulene and coronene exhibit stronger interaction energies as more curvature is introduced, except at unnaturally close intermolecular distances or high degrees of curvature. Using symmetry adapted perturbation theory (SAPT)\cite{Jeziorski:1994:1887, Szalewicz:2012:254}, we were able to determine that this stronger interaction comes from stabilizing dispersion, induction and charge penetration interactions with smaller destabilizing interactions from exchange interactions. For accurate computations on lattice energies one needs to go beyond two-body effects to three-body effects if the cluster expansion is being used. Three-body dispersion is normally a smaller fraction of the lattice energy of a crystal when compared to three-body induction. We investigated the three-body contribution using the counterpoise corrected formula of Hankins \textit{et al.}.\cite{Hankins:1970:4544} \begin{equation} \Delta ^{3} E^{ABC}_{ABC} = E^{ABC}_{ABC} - \sum_{i} E^{ABC}_{i} - \sum_{ij} \Delta ^{2} E^{ABC}_{ij}, \end{equation} where the superscript ABC represents the trimer basis and the E(subscript i) denotes the energy of each monomer, where {\em i} counts over the individual molecule of the trimer. The last term is defined as \begin{equation} \Delta ^{2} E^{ABC}_{ij} = E^{ABC}_{ij} - E^{ABC}_{i} - E^{ABC}_{j}, \end{equation} where the energies of all dimers and monomers are determined in the trimer basis. Using these formulae we investigated the three-body contribution to the lattice energy of crystalline benzene with CCSD(T). By using CCSD(T) computations we resolved a debate in the literature about the magnitude of the non-additive three-body dispersion contribution to the lattice energy of the benzene crystal. Based on CCSD(T) computations, we report a three-body dispersion contribution of 0.89 kcal mol⁻¹, or 7.2\% of the total lattice energy. This estimate is smaller than many previous computational estimates\cite{Tkatchenko:2012:236402,Grimme:2010:154104,Wen:2011:3733,vonlilienfeld:2010:234109} of the three-body dispersion contribution, which fell between 0.92 and 1.67 kcal mol⁻¹. The benchmark data we provide confirm that three-body dispersion effects cannot be neglected in accurate computations of the lattice energy of benzene. Although this study focused on benzene, three-body dispersion effects may also contribute substantially to the lattice energy of other aromatic hydrocarbon materials. Finally, density functional theory (DFT) was applied to the rate-limiting step of the hydrolytic kinetic resolution (HKR) of terminal epoxides to resolve questions surrounding the mechanism. We find that the catalytic mechanism is cooperative because the barrier height reduction for the bimetallic reaction is greater than the sum of the barrier height reductions for the two monometallic reactions. We were also able to compute barrier heights for multiple counter-ions which react at different rates. Based on experimental reaction profiles, we saw a good correlation between our barrier heights for chloride, acetate, and tosylate with the peak reaction rates reported. We also saw that hydroxide, which is inactive experimentally is inactve because when hydroxide is the only counter-ion present in the system it has a barrier height that is 11-14 kJ mol⁻¹ higher than the other three counter-ions which are extremely active.

In the research described in this thesis, two molecular layers were successfully anchored on carbon surfaces (pyrolyzed photoresist films, PPFs) sequentially through two independent approaches. The first molecular layer, styrene, was covalently bonded on PPF surfaces via the method of reduction of in situ generated diazonium ions. The resulting molecular films were characterized by AFM measurements, and catechol and ferrocyanide voltammetry. The second molecular layer, ferrocene-thiol, was anchored on top of the first molecular layer through the method of thiol-ene reaction, which is an effective method for building up multilayers through layer-by-layer assembly. As ferrocene is an electrochemically active species, quantitative surface coverage was calculated according to the amount of surface-bound ferrocene through electrochemical measurements. Finally, molecular junctions were fabricated by depositing metal top contacts based on the molecular layers through electron-beam evaporation and the electronic characteristics of these molecular junctions were investigated.

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / Tailoring the properties of a bulk material such as a pharmaceutical compound, through non-covalent interactions, could lead to the enhancement of its physical properties without chemically modifying the individual molecules themselves. In order to obtain a degree of control and reliability of these non-covalent interactions, we must develop a series of synthons - patterns of non-covalent interactions between molecules. A family a N-heterocyclic amides were synthesised and an assessment of their binding selectivities was made, by evaluation of the supramolecular yield, (the frequency of occurrence of the desired connectivities). It was found that the supramolecular yield increased with increasing basicity of the heterocyclic nitrogen atom. However, there is a point where the heterocycle becomes basic enough to produce salts, which often leads to unpredictable connectivity and stoichiometry. Once the effectiveness of the N-heterocyclic amides as supramolecular reagents was established, a series of more closely-related ditopic hydrogen-bond acceptor molecules were synthesized. The supramolecular reagents contained imidazole and pyridine binding sites, so that the two sites differ in terms of their basicity and geometry. An assessment of the ability of these molecules to induce selectivity when a hydrogen bond donor such as a cyanoxime or a carboxylic acid is introduced was made. A total of nineteen crystal structures were obtained, of which one yielded a salt with unpredictable connectivity, and eighteen were cocrystals. Ten of these were 2:1 co-crystals, which shows that the two sites are accessible for binding. Eight were 1:1 stoichiometry, with five out of eight (63%) forming a hydrogen bond to the best acceptor. In addition, a series of molecular electrostatic potential calculations were employed to investigate the binding preferences and probe the best donor/best acceptor hypothesis. A ternary supermolecule was also constructed from a central, asymmetric hydrogen-bond acceptor and two different hydrogen-bond donor molecules. It was found that the best donor, the cyanoxime, bound to the best acceptor, the imidazole nitrogen atom, while the second best donor, a carboxylic acid, bound to the second best acceptor. The calculated molecular electrostatic potential values were used to rationalize this event. A series of substituted cyanophenyloxime, hydrogen bond donor molecules were synthesized and their effectiveness at forming co-crystals was examined. It was found that simple R group substitution could have a significant effect upon the co-crystal forming ability of the hydrogen bond donors, having improved the yield from 4% and 7% in a series of co-crystallizations with closely-related oximes, to 96% with the cyanoximes. A series of di- and tritopic cyanoximes were synthesized and an assessment of their co-crystal-forming ability was made. They were found to be equally effective at producing co-crystals as the monotopic cyanoximes, having done so in 23 out of 24 cases. In contrast to their carboxylic acid counterparts, the polycyanoximes also exhibited excellent solubility. Finally, a series of ditopic ligands (N-heterocyclic amide and pyridyl cyanoximes) were employed in the synthesis of metal complexes. The amide-based ligands were found to be very effective at organizing the metal architectures with coordination through the heterocyclic nitrogen atom and propagation of one-dimensional chains through carboxamidecarboxamide interactions. These interactions prevailed even in the presence of potentially disruptive species such as solvent molecules, (in Ag(I) complexes) counterions, or other hydrogen bond acceptors. The self-complementarity of the oxime moiety was found not to prevail in any of the cases, but the pyridyl cyanoximes were consistent in their behaviour, forming an O-H…O (oxime-oxygen) hydrogen bond to a carboxylate or acac moiety.

The Effective Fragment Potential (EFP) is a quantum-mechanical based model used to describe non-covalent interactions of small molecules or fragments. It can be used along with fully <i>ab initio</i> methods to study the electronic properties of complex systems, such as solvated chromophores or proteins. For this purpose, the system is divided into two regions: one modeled with quantum mechanics and the other with EFP. The interaction between the QM region and the effective fragments has popularly been described through electrostatics and polarization only. This thesis focuses on the development of the QM/EFP exchange-repulsion term, as well as the evaluation of the dispersion term and a charge-penetration correction. The goal of is to determine how these terms can increase the accuracy of QM/EFP calculations without an increase in their computational cost.

Photophysical properties of an array of various polyaromatic hydrocarbons were benchmarked with B3LYP, M06 and B97D methods coupled with Pople and CEP-31G(d) basis sets. Results from the benchmark show the importance of diffuse basis sets when modeling the electronic properties of highly conjugated systems and provide qualitative reliable accuracy with certain levels of theory. B97D and M06 are applied to modeling pyrene adducts governed by non-covalent interactions in both gaseous and condensed states to reproduce experimental spectra. DFT calculations with both B97D and M06 functionals show qualitatively and quantitatively that pyrene dimer is a stronger π–base as compared to its monomer. Binding energies coupled with MEP, PCA and Qzz results show that the difference in π-basicity of the monomer and dimer impacts the supramolecular chemistry involved in adducts formed with super π-acidic silver cyclometallic trimer (CTC). Non-covalent interactions between coinage metal CTCs and ammonia/phosphine substrates is reported. Interactions between these substrates and the facial plane of the π-rich gold CTC reveal a novel interaction, where the typical Lewis acid/base roles are reversed for the substrates. Adducts formed through this type of interaction define typical Lewis bases like ammonia and phosphine as Lewis acids, wherein the partially positive hydrogens coordinate to the metallo-aromatic center through dipole-quadrupole interactions. Interactions of ammonia at the side positions is shown to heavily impact the Lewis basicity of the CTC facial plane leading to similar interactions exhibited by the ammonia-gold CTC adducts. Structural and electronic properties of the adducts modeled are examined.